Toward kingdom-wide analyses of gene expression

Julca, Irene; Tan, Qiao Wen; Mutwil, Marek

doi:10.1016/j.tplants.2022.09.007

Cited by 24 publications

(25 citation statements)

References 99 publications

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“…Transcription retains a leading role for the understanding of gene functions and the discovery of biological pathways involved in plant evolution and crop improvement [ 114 ]. Transcriptomic technologies are growing rapidly and their progress in terms of sensitivity and cost-effectiveness has resulted in a great expansion of gene expression publicly available data [ 2 ].…”

Section: Comparative and Integrative Approaches For Data Exploitationmentioning

confidence: 99%

A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation

Zuluaga

Blanco

Mangini

et al. 2023

Plants

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Durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) is an allotetraploid cereal crop of worldwide importance, given its use for making pasta, couscous, and bulgur. Under climate change scenarios, abiotic (e.g., high and low temperatures, salinity, drought) and biotic (mainly exemplified by fungal pathogens) stresses represent a significant limit for durum cultivation because they can severely affect yield and grain quality. The advent of next-generation sequencing technologies has brought a huge development in transcriptomic resources with many relevant datasets now available for durum wheat, at various anatomical levels, also focusing on phenological phases and environmental conditions. In this review, we cover all the transcriptomic resources generated on durum wheat to date and focus on the corresponding scientific insights gained into abiotic and biotic stress responses. We describe relevant databases, tools and approaches, including connections with other “omics” that could assist data integration for candidate gene discovery for bio-agronomical traits. The biological knowledge summarized here will ultimately help in accelerating durum wheat breeding.

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Section: Comparative and Integrative Approaches For Data Exploitationmentioning

confidence: 99%

A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation

Zuluaga

Blanco

Mangini

et al. 2023

Plants

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“…With the development of high-throughput sequencing technology, plant RNA-seq datasets can be obtained rapidly and comprehensively [ 24 , 25 ]. This technology is now widely used in transcriptome gene expression analysis [ 26 ], secondary metabolism studies of plants [ 27 , 28 ], disease resistance mechanisms [ 29 ], biocontrol [ 30 , 31 ], and so on. RNA-seq datasets can also be used to study the molecular function of specific genes and to screen for internal reference genes [ 32 , 33 ].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata

Wang

Qian

Geng

et al. 2023

Genes

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Lamiophlomis rotata (Benth.) Kudo is a perennial and unique medicinal plant of the Qinghai–Tibet Plateau. It has the effects of diminishing inflammation, activating blood circulation, removing blood stasis, reducing swelling, and relieving pain. However, thus far, reliable reference gene identifications have not been reported in wild L. rotata. In this study, we identified suitable reference genes for the analysis of gene expression related to the medicinal compound synthesis in wild L. rotata subjected to five different-altitude habitats. Based on the RNA-Seq data of wild L. rotata from five different regions, the stability of 15 candidate internal reference genes was analyzed using geNorm, NormFinder, BestKeeper, and RefFinder. TFIIS, EF-1α, and CYP22 were the most suitable internal reference genes in the leaves of L. rotata from different regions, while OBP, TFIIS, and CYP22 were the optimal reference genes in the roots of L. rotata. The reference genes identified here would be very useful for gene expression studies with different tissues in L. rotata from different habitats.

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“…Multi-omics methods, consisting of a combination of transcriptomics, metabolomics, genomics and/or proteomics, have been utilized in the drug discovery process and have been recognized as a useful tool to identify new targets and the mechanisms of lead compounds (Goff et al, 2020). The multi-omics strategy may also be used to discover plant metabolic genes and pathways using co-expression analysis and metabolite-based genome-wide association studies (Zhan et al, 2022;Zhao and Rhee, 2022;Julca et al;Lim et al, 2022;Usadel et al, 2009). Taken together, such multi-omics approaches may represent the means to address challenges associated with bioprospecting and bridge the knowledge gap.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and metabolomic characterization of antibacterial activity ofMelastoma dodecandrum

Poh

Ruhazat

Yang

et al. 2023

Preprint

Self Cite

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Antibacterial resistance poses a significant global threat, necessitating the discovery of new therapeutic agents. Plants are a valuable source of secondary metabolites with demonstrated anticancer and antibacterial properties. In this study, we reveal that Melastoma dodecandrum exhibits both bacteriostatic and bactericidal effects against Pseudomonas aeruginosa and Staphylococcus aureus. Treatment with plant extracts results in membrane damage and a reduction in Pseudomonas swimming and swarming motility. A comparative analysis of bacterial transcriptomes exposed to Melastoma extracts and four distinct antibiotics indicates that the extracts trigger similar transcriptomic responses as triclosan, a fatty acid inhibitor. Activity-guided fractionation suggests that the antibacterial activity is not attributable to hydrolyzable tannins, but to unidentified minor compounds. Additionally, we identified 104 specialized metabolic pathways and demonstrated a high level of transcriptional coordination between these biosynthetic pathways and phytohormones, highlighting potential regulatory mechanisms in plant metabolism.

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Toward kingdom-wide analyses of gene expression

Cited by 24 publications

References 99 publications

A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation

A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation

Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata

Transcriptomic and metabolomic characterization of antibacterial activity ofMelastoma dodecandrum

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